- Fall 2016, Tuesdays and Thursdays 12:25–1:45pm at WEB 2230
- Teaching Assistants (TAs): Cody and Amanda
- Graders: Kyle and Ashley
- TA Office Hours: Mondays and Wednesdays 2:00–4:00pm at WEB 1460, and Tuesdays and Thursdays 4:00–6:00pm at WEB 1450
- Staff Meetings: Mondays 4:00–5:00pm at WEB 3840

- Syllabus

- What additional skills will we gain and how will we do it?

- 100% grade = 60% assignments, 30% quizzes, 10% class participation; assignments and quizzes require cover page (-10%), and accepted up to two days late (-10%/day); class attendance is required.

- Required Textbook: Principles of Statistics, by Bulmer, Dover (1979).
- Optional Textbook: Introduction to Probability, by Freund, Dover (1973).
- Required Software: Download a Mathematica license for your laptop for as low as $50, or get a trial version.

- Tutoring
- Important Dates
- Safety
- Health, Wellness, and Counseling
- Code of Student's Rights and Responsibilities

- Aug 23:
- Formulate an approach for solving a combinatorial problem of a known solution that demonstrates that 0! must equal a specific number for mathematical consistency. What is that number? This is a combinatorial proof that 0!=...
- Bacteriophage lambda, a bacterial virus, has a double-stranded circular DNA genome, containing roughly 65 genes. How many possibilities are there to arrange the genes into the circular genome?
- Human chromosome 2, the second largest human chromosome, contains roughly 2,000 protein-encoding genes. There is evidence that this human chromosome arose from the fusion of two ancestral ape chromosomes, homologous to chromosomes 2A and 2B in the chimpanzee with roughly 1,000 genes each. How many possibilities are there to arrange two groups of 1,000 genes into a chromosome of 2,000 genes?
- In a single throw of a die, what is the probability to get a number that is divisible by 2 OR 3? 2 AND 3?
- In a single throw of a die, what is the probability to get a number that is divisible by 3 OR 6? 3 AND 6?
- Is independence mutual?
- Does independence imply mutual exclusiveness?
- Does mutual exclusiveness imply independence?
- Paper 1: A Correlation of Cytological and Genetical Crossing-Over in
*Zea mays*, by Creighton and McClintock,*PNAS*(1931). - Paper 2: Systematic Determination of Genetic Network Architecture, by Tavazoie et al.,
*Nat Genet*(1998). - Paper 3: GSVD Comparison of Patient-Matched Normal and Tumor aCGH Profiles Reveals Global Copy-Number Alterations Predicting Glioblastoma Multiforme Survival, by Lee et al.,
*PLoS One*(2012). - Paper 4: Lung Cancer and Cigarettes?, by Fisher,
*Nature*(1958). - Paper 5: The World of Smoking Guns, by Sen,
*Tob Control*(2007). - Paper 6: Increased Genetic Vulnerability to Smoking at
*CHRNA5*in Early-Onset Smokers, by Hartz et al.,*JAMA Psychiatry*(2012). - For a given set of observations, show that the mean minimizes the variance.
- What are the average and variance of the binomial distribution?
- What are the average and variance of the hypergeometric distribution?
- What is the probability for 79 heads in 79 coin flips?
- What is the p-value of 79 heads in 79 coin flips?
- How would you interpret a p-value << 1 in this case?
- Paper 7: Mutations of Bacteria from Virus Sensitivity
to Virus Resistance, by Luria and Delbrück,
*Genetics*(1943). - Paper 8: One Hundred Years of Light Quanta, by Glauber,
*Rev Mod Phys*(2006). - How to compare an observed distribution with an expected distribution?
- How to compare two observed distributions?
- Paper 9: Real-Time Tracking of Non-Rigid Objects using Mean Shift, by Comaniciu et al.,
*IEEE CVPR*(2000). - Patent 1: Real-Time Tracking of Non-Rigid Objects using Mean Shift, by Comaniciu and Ramesh,
*US Patent*(2003). - Paper 10: Sparsity Control for Robust Principal Component Analysis, by Mateos and Giannakis,
*IEEE Asilomar*(2010). - Paper 11: Robust Principal Component Analysis?, by Candès et al.,
*J ACM*(2011). - Paper 12: On the Movement of Small Particles Suspended in a Stationary Liquid Demanded by the Molecular Kinetic Theory of Heat, by Einstein,
*Ann Phys*(1905). - Paper 13: Brownian Movement and Molecular Reality, by Perrin,
*Ann Chim Phys*(1909). - Paper 14: Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition, by Aiello and Alter,
*PLoS One*(2016). - Paper 15: Nonparametric Estimation from Incomplete Observations, by Kaplan and Meier,
*J Am Statist Assoc*(1958). - Paper 16: Clinical Development Success Rates for Investigational Drugs, by Hay,
*Nat Biotechnol*(2014).

- Welcome!

- Data Science in the News

- Big Data's High Priests of Algorithms from the Wall Street Journal

- Data Science: The Numbers of Our Lives from the New York Times

- NSA Keeping Details about Data Center Quiet from KSL

- How to Catch a Criminal with Data from the Atlantic Monthly

- How Companies Learn Your Secrets from the New York Times

- I.B.M.: Big Data, Bigger Patterns from the New York Times

- The Age of Big Data from the New York Times

- For Today's Graduate, Just One Word: Statistics from the New York Times

- Most Lucrative College Degrees from CNN

- If You Liked This, You're Sure to Love That from the New York Times

- Assignment 1: Combinatorics

- Due In-Class Sept 6

- Combinatorics: Counting Permutations and Selecting Subsets with Factorials and Binomial Coefficients

- Class Notes 1

- Genome Rearrangements:

Aug 25:

- The Binomial Theorem and Pascal's Triangle

- Class Notes 2

- The Binomial Theorem from Wikipedia

- Pascal's Triangle from Wikipedia

- P vs. NP Problem from the Clay Institute

- The Millennium Prize Problems from the Clay Institute

- Grigori Perelman from Wikipedia

Aug 30:

- Guest Lecture: Risk and Reward – Lies, Damned Lies, and Statistics

Glenn D. Prestwich, Presidential Professor of Medicinal Chemistry

- Hosts: Brandon and Madison

- Extra Credit Participation 1: Prepare a "Thank You" note for Prof. Prestwich.

- Due In-Class Sept 6

Sept 1:

- In-Class Work with the TAs on Assignment 1

Sept 6:

- Introduction to Mathematica, Part I

- Class Notes 3

- In-Class Project 1: Traveling Salesman Problem (TSP) Utah Style

- Download to your desktop the executable Mathematica 9.0.1 code: In-Class_Project_1.nb

- Download the tab-delimited text file: Utah_Driving_Distances.txt

- The Traveling Salesman Problem from Mathworld

- The Traveling Salesman Problem from xkcd

- Assignment 2: Probabilities

- Due In-Class Sept 20

- It's My Birthday Too, Yeah from the New York Times

Sept 8:

- Introduction to Mathematica, Part II

- Class Notes 4

Sept 13:

- In-Class Work with the TAs on Assignment 2

Sept 15:

- From Combinatorics to Probability: The Law of Addition and the Law of Multiplication

From Bulmer (Dover 1979), pp. 13–22.

- Class Notes 5

- Class Notes 6

- Mendel's Laws of Heredity: Statistics Predicts the Existence of Chromosomes

From Bulmer (Dover 1979), pp. 22–25.

- The Nobel Prize in Physiology or Medicine 1983 Barbara McClintock

- Genetic Recombination, by Clancy,

Sept 20:

- Pop Quiz

- From Combinatorics to Probability Distributions: Deriving the Hypergeometric and the Binomial Distributions

- Class Notes 7

- The Hypergeometric Distribution from Wikipedia

- The Hypergeometric Distribution from Mathworld

- Assignment 3: The P-Value and Probability Distributions

- Download to your desktop the executable Mathematica 9.0.1 code: Assignment_3.nb

- Due In-Class Oct 4

Sept 22:

- From Probability to Statistics: The P-Value

- Class Notes 8

- The P-Value from Wikipedia

- High-Throughput Biotechnologies

- Assessing Significance in Large-Scale Molecular Biological Data:

Sept 27:

- Quiz 1 Preparation, Part I

- Class Notes 9

- Class Notes 10

- Discovery and Types of Genetic Linkage, by Lobo and Shaw (

- The Binomial Distribution from Wikipedia

- The Binomial Distribution from Mathworld

Sept 29:

- Guest Lecture: Genetics, Statistics and Smoking: Lessons in Cause and Effect

Robert B. Weiss, Professor of Human Genetics

- Hosts: Ari, Patrick, and Youngjae

- The Nobel Prize in Economics 1998
Amartya Sen

- Extra Credit Participation 2: Prepare a "Thank You" note for Prof. Weiss.

- Due In-Class Oct 4

Oct 4:

- Quiz 1 Preparation, Part II

- Class Notes 11

Oct 6:

- Quiz 1

- Assignment 4: Simulations of the Binomial Distribution

- Download to your desktop the executable Mathematica 9.0.1 code: Assignment_4.nb

- Due In-Class Oct 27

Oct 11:

- Happy Fall Break!

Oct 13:

- Happy Fall Break!

Oct 18:

- Mean, Variance, and Correlation, Part I

From Bulmer (Dover 1979), pp. 68–75.

- Class Notes 12

Oct 20:

- Mean, Variance, and Correlation, Part II: Intuitively Obvious to the Most Casual Observer?

- Class Notes 13

- Class Notes 14

- 79 Coin Flips from Rosencrantz and Guildenstern are Dead

- The Unbiased Binomial Distribution from The Simpsons

- Galton Board from Mathworld

- The Bean Machine from Wikipedia

Oct 25:

- The Poisson Distribution and the Statistics of Natural Processes

From Bulmer (Dover 1979), pp. 90–96.

- Class Notes 15

Oct 27:

- The Luria-Delbrück Experiment: Statistics Proves the Occurrence of Random Genetic Mutations

- Class Notes 16

- The Nobel Prize in Physiology or Medicine 1969
Max Delbrück, Alfred D. Hershey, Salvador E. Luria

- The Luria-Delbrück Experiment from Wikipedia

- In-Class Project 2: Mean, Variance, and the Poisson Distribution

- Download to your desktop the executable Mathematica 9.0.1 code: In-Class_Project_2.nb

- Assignment 5: The Poisson Distribution and Symbolic Computations

- Download to your desktop the executable Mathematica 9.0.1 code: Assignment_5.nb

- Due In-Class Nov 10

Nov 1:

- Poisson Distribution and Quantum Mechanics

- Class Notes 17

- The Nobel Prize in Physics 2005 Roy J. Glauber, John L. Hall, Theodor W. Hänsch

- Photon Number Distributions from Wolfram Demonstrations

- For example: The Chi-Squared Test of Goodness of Fit from Bulmer (Dover 1979), pp. 154–161.

- Pearson's Chi-Squared Test from Wikipedia

- Genetics and Statistical Analysis, by Lobo (

- In-Class Project 3: Chi-Squared Test of Goodness of Fit

- Download to your desktop the executable Mathematica 9.0.1 code: In-Class_Project_3.nb

- For example: The Bhattacharyya Coefficient from Wikipedia

- In-Class Project 4: Bhattacharyya Coefficient Measure

- Download to your desktop the executable Mathematica 9.0.1 code: In-Class_Project_4.nb

Nov 3:

- Bayes’ Theorem, Conditional Probability and the Law of Multiplication from Wikipedia

- The Mathematics of Changing Your Mind from the New York Times

- Monty Hall Problem from Wikipedia

- Monty Hall from xkcd

Extra Credit Activity, Monday, Nov 7 at 4:00–5:00pm at LCB 222

- Department of Mathematics Applied Mathematics Seminar:
Cancer Diagnostics and Prognostics from Comparative Spectral Decompositions of Patient-Matched Genomic Profiles

Orly Alter

Nov 8:

- Vote!

- Gaussian Function, Normal Distribution and Random Walk

- Class Notes 18

- Gaussian Function from Mathworld

- Normal Distribution from Wikipedia

- One-Dimensional Random Walk from Mathworld

Nov 10:

- Take Home Quiz 2

- Due In-Class Dec 8

- Class Notes 19

- Assignment 6: Random Walk, Normal Distribution, and Brownian Motion; Linear Regression and the Method of Least Squares

- Download to your desktop the executable Mathematica 9.0.1 code: Assignment_6.nb

- By Invitation, Due In-Class Dec 8

Nov 15:

- Brownian Motion: Statistics Proves the Atomic Nature of Matter

- Brownian Motion from Wikipedia

- The Nobel Prize in Physics 1921
Albert Einstein

- The Nobel Prize in Physics 1926
Jean Baptiste Perrin

Extra Credit Activity, Wednesday, Nov 16 at 1:00–5:00pm at WEB, 3rd and 4th floors

- SCIx: Scientific Computing and Imaging Institute Open House

Nov 17:

- Linear Regression and the Method of Least Squares from Bulmer (Dover 1979), pp. 210–215.

- Coefficient of Determination from Wikipedia

- Kepler's Laws of Planetary Motion from Wikipedia

- In-Class Project 5: Kepler's Third Law of Planetary Motion

- Download to your desktop the executable Mathematica 9.0.1 code: In-Class_Project_5.nb

Nov 22:

- Katie Aiello of the University of Utah on Computing for Brain Cancer Treatment from "Why Compute?" by L. McIver

- Advanced Topics: Survival Analysis, Part I

- Download to your desktop the executable Mathematica 9.0.1 code: Advanced_Topics-Survival_Analysis.nb

- Download the tab-delimited text file: Toy_Data.txt

- Download the tab-delimited text file: 251_Patients.txt

Nov 24:

- Happy Thanksgiving!

Nov 29:

- In-Class Work with the TAs on Quiz 2 and Assignment 6

Dec 1:

- Safety Presentation

Dec 6:

- In-Class Work with the TAs on Quiz 2 and Assignment 6

Dec 8:

- End-of-Class Celebration!

- Advanced Topics: Survival Analysis, Part II

- The Data Vigilante from the Atlantic Monthly

- How Bright Promise in Cancer Testing Fell Apart from the New York Times

Happy Winter Break!

- DNA from xkcd

- See you in Spring 2017 in BIOEN 6770: Genomic Signal Processing